The present invention relates to polypeptides produced in yeast, a DNA construct comprising a DNA sequence encoding such polypeptides, vectors carrying such DNA fragments and yeast cells transformed with the vectors, as well as a process of producing heterologous proteins in yeast.
Yeast organisms produce a number of proteins synthesized intracellularly, but having a function outside the cell. Such extracelluar proteins are referred to as secreted proteins. These secreted proteins are expressed initially inside the cell in a precursor or a pre-form containing a pre-peptide sequence ensuring effective direction of the expressed product across the membrane of the endoplasmic reticulum (ER). The pre-peptide, normally named a signal peptide, is generally cleaved off from the desired product during translocation. Once entered in the secretory pathway, the protein is transported to the Golgi apparatus. From the Golgi the protein can follow different routes that lead to compartments such as the cell vacuole or the cell membrane, or it can be routed out of the cell to be secreted to the external medium (Pfeffer et al. (1987) Ann. Rev. Biochem. 56:829-852).
Several approaches have been suggested for the expression and secretion in yeast of proteins heterologous to yeast. European publication 088632A describes a process by which proteins heterologous to yeast are expressed, processed and secreted by transforming a yeast organism with an expression vector harbouring DNA encoding the desired protein and a signal peptide, preparing a culture of the transformed organism, growing the culture and recovering the protein from the culture medium. The signal peptide may be the desired protein""s heterologous signal peptide, or a hybrid of a homologous and a heterologous signal peptide.
A problem encountered with the use of signal peptides heterologous to yeast may be that the heterologous signal peptide does not ensure efficient translocation and/or cleavage after the signal peptide.
The Saccharomyces cerevisiae MFxcex11 (xcex1-factor) is synthesized as a pre-pro form of 165 amino acids comprising a 19 amino acids long signal- or pre-peptide followed by a 64 amino acids long xe2x80x9cleaderxe2x80x9d or pro-peptide, (Kurjan et al. (1982) Cell 30:933-943). Use of signal/leader peptides homologous to yeast is described in U.S. Pat. No. 4,546,082; EP publications 0116201A, 0123294A, 0123544A, 0163529A, 0123289A, EP No. 0100561B, and PCT Publication WO 95/02059.
In EP 0123289A utilization of the S. cerevisiae xcex1-factor precursor is described whereas EP 0100561 describes the utilization of the S. cerevisiae PHO5 signal and WO 95/02059 describes the utilization of YAP3 signal peptide for secretion of foreign proteins.
U.S. Pat. No. 4,546,082 and European Publication Nos. 0016201A, 0123294A, 0123544A and 0163529A describe processes by which the xcex1-factor signal-leader from S. cerevisiae (MFxcex11 or MFxcex12) is utilized in the secretion process of expressed heterologous proteins in yeast. Secretion and processing of the desired protein was demonstrated by fusing a DNA sequence encoding the S. cerevisiae MFxcex11 signal/leader peptide at the 5xe2x80x2 end of the gene for the desired protein.
EP 0206783 discloses a system for the secretion of polypeptides from S. cerevisiae whereby the xcex1-factor signal/leader sequence has been truncated to eliminate the four xcex1-factor peptides present on the native sequence so as to leave the signal/leader peptide itself fused to a heterologous polypeptide via the xcex1-factor processing site Lys-Arg-Glu-Ala-Glu-Ala (SEQ ID NO:93). It is indicated that this construction leads to an efficient process for production of smaller peptides (less than 50 amino acids). For the secretion and processing of larger polypeptides, the native xcex1-factor leader sequence has been truncated to leave one or two xcex1-factor peptides between the leader peptide and the polypeptide.
A number of secreted proteins are routed so that the precursor is exposed to a proteolytic processing system which can cleave the peptide bond at the carboxy end of two consecutive basic amino acids. This enzymatic activity is in S. cerevisiae encoded by the KEX 2 gene (Julius et al. (1984) Cell 37:1075). Processing of the product by the KEX 2 protease is needed for the secretion of active S. cerevisiae mating factor xcex11 (MFxcex11 or xcex1-factor) but is not involved in the secretion of active S. cerevisiae mating factor a.
Secretion and correct processing of a polypeptide intended to be secreted is obtained in some cases when culturing a yeast organism which is transformed with a vector constructed as indicated in the references given above. In many cases, however, the level of secretion is very low or there is no secretion, or the proteolytic processing may be incorrect or incomplete. As described in WO 90/10075, this is believed to be ascribable, to some extent, to an insufficient exposure of the processing site present between the C-terminal end of the leader peptide and the N-terminal end of the heterologous protein so as to render it inaccessible, or less accessible, to proteolytic cleavage, for example, by the KEX 2 protease.
WO 90/10075 describes a yeast expression system with improved processing of a heterologous polypeptide obtained by providing certain modifications near the processing site at the C-terminal end of the leader peptide and/or the N-terminal end of a heterologous polypeptide fused to the leader peptide.
The present invention describes modifications of the N-terminal end of the heterologous polypeptide designed as extensions which can be cleaved off either by naturally occurring yeast proteases before purification from the culture media or by in vitro proteolysis during or subsequently to purification of the product from the culture media.
In one aspect, the present invention is drawn to a DNA construct encoding a polypeptide having the structure:
signal peptide-leader peptide-X1-X2-X3-X4X5-X6-X7-heterologous protein
wherein
X1 is Lys or Arg;
X2 is Lys or Arg, X1 and X2 together defining a yeast processing site;
X3 is Glu or Asp;
X4 is a sequence of amino acids with the following structure
(A-B)n
wherein A is Glu or Asp, B is Ala, Val, Leu or Pro, and n is 0 or an integer from 1 to 5, and when nxe2x89xa72 each A and B is the same or different from the other A(s) and B(s); or
X4 is a sequence of amino acids with the following structure
(C)m
wherein C is Glu or Asp, and m is 0 or an integer from 1 to 5;
X5 is a peptide bond or is one or more amino acids which may be the same or different;
X6 is a peptide bond or an amino acid residue selected from the group consisting of Pro, Asp, Thr, Glu, Ala and Gly; and
X7 is Lys or Arg.
A specific embodiment of the present invention is drawn to a DNA construct encoding a polypeptide having the structure:
signal peptide-leader peptide-X1-X2-X3-X4-X5-X6-X7-heterologous protein
wherein X3-X4-X5-X6-X7 are the sequence Glu Glu Ala Glu Pro Lys (SEQ ID NO: 1).
The sequence Glu Glu Ala Glu Pro Lys (SEQ ID NO: 1) forms an extension at the N-terminal of the heterologous polypeptide. This extension not only increases the fermentation yield but is protected against dipeptidyl aminopeptidase (DPAP A) processing, resulting in a homogenous N-terminal of the polypeptide. The extension is constructed in such a way that it is resistant to proteolytic cleavage during fermentation so that the N-terminally extended heterologous protein product can be purified from the culture media for subsequent in vitro maturation, e.g. by trypsin or Achromobacter lyticus protease I. The desired in vitro removal of the N-terminal extension of SEQ ID NO:1 is readily achieved by either trypsin or Achromobacter lyticus protease I, presumably due to flexibility of the N-terminal extension peptide resulting in an improved yield of the matured heterologous protein.
Another specific embodiment of the present invention is drawn to a DNA construct encoding a polypeptide having the structure:
signal peptide-leader peptide-X1-X2-X3-X4-X5-X6-X7-heterologous protein
wherein X3-X4-X5-X6-X7 are the sequence Glu Glu Gly Glu Pro Lys (SEQ ID NO:2).
The sequence Glu Glu Gly Glu Pro Lys (SEQ ID NO:2) forms an extension at the N-terminal of the heterologous polypeptide. Without being bound by any specific theory, it is surprising shown that the location of a glycine (G) in the N-terminal extension compared to the repeated Glu Ala of the xcex1-factor leader results in improved heterologous protein yield which may reflect an improved translocation and/or secretion, since glycine with only a hydrogen atom as a side chain can adopt a much wider range of conformations than other amino acid residues, thus allowing unusual main chain conformations, and a possible more unstable precursor polypeptide and secretion process.
The term xe2x80x9csignal peptidexe2x80x9d is understood to mean a pre-peptide which is present as an N-terminal sequence on the precursor form of an extracellular protein expressed in yeast. The function of the signal peptide is to allow the heterologous protein to be secreted to enter the endoplasmic reticulum. The signal peptide is normally cleaved off in the course of this process. The signal peptide may be heterologous or homologous to the yeast organism producing the protein. A preferred signal peptide in this invention is yeast aspartic protease 3 (YAP3) signal peptide or any functional analogue thereof. YAP 3 has been cloned and characterised by Egel-Mitani et al. (1990) YEAST 6:127-137.
The term xe2x80x9cleader peptidexe2x80x9d means a polypeptide sequence whose function is to allow the heterologous protein to be secreted to be directed from the endoplasmic reticulum to the Golgi apparatus and further to a secretory vesicle for secretion into the medium. Preferably the leader peptide used in the present invention is selected from the following group of leader peptides
Gln Pro Ile Asp Glu Asp Asn Asp Thr Ser Val Asn Leu Pro Ala (SEQ ID NO:3);
Gln Pro Ile Asp Asp Glu Asn Thr Thr Ser Val Asn Leu Pro Ala (SEQ ID NO:4);
Gln Pro Ile Asp Asp Glu Ser Asn Thr Thr Ser Val Asn Leu Pro Ala(SEQ ID NO:5);
Gln Pro Ile Asp Asp Glu Asn Thr Thr Ser Val Asn Leu Pro Val (SEQ ID NO:6);
Gln Pro Ile Asp Asp Thr Glu Asn Thr Thr Ser Val Asn Leu Pro Ala (SEQ ID NO:7);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Pro Ala (SEQ ID NO:8);
Gln Pro Ile Asp Asp Glu Asn Thr Thr Ser Val Asn Leu Met Ala (SEQ ID NO:9);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Pro Gly Ala (SEQ ID NO:10);
Gln Pro Ile Asp Asp Thr GIu Ser Asn Thr Thr Ser Val Asn Leu Met Ala (SEQ ID NO:11);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Val Pro Thr (SEQ ID NO:12;
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Leu Val Asn Val Pro Thr (SEQ ID NO:13;
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Pro Thr (SEQ ID NO:14);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Leu Val Asn Val Pro Gly Ala (SEQ ID NO:15);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Pro Ala Val Ala (SEQ ID NO:16);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Asp Leu Ala Val Gly Leu Pro Gly Ala (SEQ ID NO:17);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Ile Asn Thr Thr Leu Val Asn Leu Pro Gly Ala (SEQ ID NO:18);
Gln Pro Ile Asp Asp Thr Glu Ser Ile Asn Thr Thr Leu Val Asn Leu Pro Gly Ala (SEQ ID NO:19);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Leu Val Asn Leu Pro Gly Ala (SEQ ID NO:20);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Val Asn Leu Pro Leu (SEQ ID NO:21);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Ile Asn Thr Thr Leu Val Asn Leu Ala Asn Val Ala Met Ala (SEQ ID NO:22);
Gln Pro Ile Asp Asp Thr Glu Ser Ala Ile Asn Thr Thr Leu Val Asn Leu Pro Gly Ala (SEQ ID NO:23);
Gln Pro Ile Asp Asp Thr Glu Ser Phe Ala Thr Asn Thr Thr Leu Val Asn Leu Pro Gly Ala (SEQ ID NO:24);
Gln Pro Ile Asp Asp Thr Glu Ser Ile Asn Thr Thr Leu Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Val Asn Leu Pro Leu (SEQ ID NO:25);
Gln Pro Ile Asp Asp Thr Glu Ser Ile Asn Thr Thr Leu Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Asp Val Val Asn Leu Pro Gly Ala (SEQ ID NO:26);
Gln Pro Ile Asp Asp Thr Glu Ser Ala Ala Ile Asn Thr Thr Leu Val Asn Leu Pro Gly Ala (SEQ ID NO:27);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Val Asn Leu Ala Asn Val Ala Met Ala (SEQ ID NO:28);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Asp Val Val Asn Leu Ile Ser Met Ala (SEQ ID NO:29);
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asn Thr Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Asp Val Val Asn Leu Ile Ser Met Ala (SEQ ID NO:30);
identified in PCT/DK95/00249 and all C-terminally followed by a Lys-Arg sequence and any functional analogue thereof, and more preferably the leader peptide has an amino acid sequence of 43 or more amino acids, such as the leader peptide (LA19):
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Ala Leu Asp Val Val Asn Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:31),
identified in PCT/DK95/00249 and which includes the C-terminal Lys-Arg processing site, or any functional analogue thereof. In the DNA construct of the present invention the leader peptide preferably contains an endopeptidase processing site at the C-terminal end, such as a Lys-Arg sequence.
Even more preferred leader peptides encoded by the DNA constructs of the invention are:
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Ala Gly Gly Leu Asp Val Val Asn Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:32),
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Ala Phe Ala Thr Asn Thr Thr Leu Ala Leu Asp Val Val Asn Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:33),
Ser Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Ala Leu Asp Val Val Asn Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:34),
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Asn Ser Gly Gly Leu Asp Val Val Asn Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:35),
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Ser Val Gly Gly Leu Asp Val Val Asn Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:36),
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Arg Phe Ala Thr Asn Thr Thr Leu Ala Gly Gly Leu Asp Val Val Gly Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:37),
Gln Pro Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Ala Phe Ala Thr Asn Thr Thr Ser Val Gly Gly Leu Asp Val Val Gly Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:38),
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Ala Phe Ala Thr AsnThr Thr Leu Ala Gly Gly Leu Asp Val Val Asn Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:39),
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Ala Phe Ala Thr Asn Thr Thr Asn Ser Gly Gly Leu Asp Val Val Asn Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:40),
Gln Pro Ile Asp Asp Thr Glu Ser Asn Thr Thr Ser Val Asn Leu Met Ala Asp Asp Thr Glu Ser Ala Phe Ala Thr Asn Thr Thr Leu Ala Gly Gly Leu Asp Val Val Gly Leu Ile Ser Met Ala Lys Arg (SEQ ID NO:41).
The term xe2x80x9cheterologous proteinxe2x80x9d means a protein or polypeptide which is not produced by the host yeast organism in nature.
In a still further aspect, the invention relates to a process for producing a heterologous protein in yeast, comprising cultivating the transformed yeast strain in a suitable medium to obtain expression and secretion of the heterologous protein, after which the protein is isolated from the medium.
The invention further relates to a recombinant expression vector which is capable of replicating in a eucaryotic cell, preferably a yeast cell, and which carries a DNA construct of the invention. Preferably, the DNA construct comprises a synthetic leader peptide, preferably the LA19 leader peptide. Besides, the invention relates to the DNA construct described in FIG. 2 herein. The invention also relates to a eucaryotic cell, preferably a yeast cell, which is capable of expressing a heterologous protein and which is transformed with a vector of the invention.